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Structural and mechanistic insight into stem‐loop RNA processing by yeast Pichia stipitis Dicer
Author(s) -
Chan JingRu,
Qinqin Fu,
Jianwei Li,
Ying Chen,
Machida Satoru,
Wei Chen,
Yuan Yuren Adam,
Jobichen Chacko
Publication year - 2021
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.4086
Subject(s) - dicer , rna , rnase p , rna silencing , ribonuclease iii , biology , microbiology and biotechnology , rna binding protein , stem loop , rnase mrp , riboswitch , non coding rna , biochemistry , rna interference , gene
Dicer is a member of the ribonuclease III enzyme family and processes double‐stranded RNA into small functional RNAs. The variation in the domain architecture of Dicer among different species whilst preserving its biological dicing function is intriguing. Here, we describe the structure and function of a novel catalytically active RNase III protein, a non‐canonical Dicer ( Ps DCR1), found in budding yeast Pichia stipitis . The structure of the catalytically active region (the catalytic RNase III domain and double‐stranded RNA‐binding domain 1 [dsRBD1]) of DCR1 showed that RNaseIII domain is structurally similar to yeast RNase III (Rnt1p) but uniquely presents dsRBD1 in a diagonal orientation, forming a catalytic core made of homodimer and large RNA‐binding surface. The second dsRNA binding domain at C‐terminus, which is absent in Rnt1, enhances the RNA cleavage activity. Although the cleavage pattern of Ps DCR1 anchors an apical loop similar to Rnt1, the cleavage activity depended on the sequence motif at the lower stem, not the apical loop, of hairpin RNA. Through RNA sequencing and RNA mutations, we showed that RNA cleavage by Ps DCR1 is determined by the stem‐loop structure of the RNA substrate, suggesting the possibility that stem‐loop RNA‐guided gene silencing pathway exists in budding yeast.